EHV-1 Gene dynamics (TSS ~ TES)
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Normalization: VST
Gene dynamics (TSS ~ TES)
Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)
When counting with either adapters, the clustering grouped ORF64 together with two late genes
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.2)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 2: 1 ORF4 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 3: 1 ORF7 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 4: 1 ORF9 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 5: 1 ORF17 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 6: 1 ORF18 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 7: 1 ORF20 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 8: 1 ORF21 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 9: 1 ORF24 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 10: 1 ORF28 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 11: 1 ORF31 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 12: 1 ORF32 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 13: 1 ORF34 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 14: 1 ORF38 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 15: 1 ORF50 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 16: 1 ORF61 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 17: 1 ORF64_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 18: 1 ORF67_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 19: 1 ORF74 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 20: 1 ORF75 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 21: 1 NOIR_2 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 22: 2 ORF2 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 23: 2 ORF3 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 24: 2 ORF8 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 25: 2 ORF11 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 26: 2 ORF19 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 27: 2 ORF22 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 28: 2 ORF26 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 29: 2 ORF29 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 30: 2 ORF36 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 31: 2 ORF37 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 32: 2 CTO 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 33: 2 ORF40 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 34: 2 ORF51 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 35: 2 ORF66_1 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 36: 2 ORF73 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 37: 2 ORF76 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 38: 3 ORF5 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 39: 3 ORF30 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 40: 3 ORF53 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 41: 3 ORF63 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 42: 3 ORF65_1 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 43: 3 ORF69 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 44: 4 ORF6 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 45: 4 ORF13 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 46: 4 ORF15 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 47: 4 ORF16 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 48: 4 ORF25 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 49: 4 ORF33 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 50: 4 ORF35.5 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 51: 4 ORF42 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 52: 4 ORF43 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 53: 4 ORF46 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 54: 4 ORF52 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 55: 4 ORF54 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 56: 4 ORF58 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 57: 4 ORF60 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 58: 4 ORF62 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 59: 4 ORF72 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 60: 5 ORF10 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 61: 5 ORF12 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 62: 5 ORF14 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 63: 5 ORF23 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 64: 5 ORF27 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 65: 5 ORF35 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 66: 5 ORF39 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 67: 5 ORF41 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 68: 5 ORF44 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 69: 5 ORF48 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 70: 5 ORF49 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 71: 5 ORF57 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 72: 5 ORF59 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 73: 5 NOIR_1 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 74: 5 ORF68 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 75: 5 ORF70 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 76: 5 ORF71 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.005240502 -0.3857226 0.2263551 0.4554380
## 2: 0.005240502 -0.3857226 0.2263551 0.4554380
## 3: 0.005240502 -0.3857226 0.2263551 0.4554380
## 4: 0.005240502 -0.3857226 0.2263551 0.4554380
## 5: 0.005240502 -0.3857226 0.2263551 0.4554380
## 6: 0.005240502 -0.3857226 0.2263551 0.4554380
## 7: 0.005240502 -0.3857226 0.2263551 0.4554380
## 8: 0.005240502 -0.3857226 0.2263551 0.4554380
## 9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.005240502 -0.3857226 0.2263551 0.4554380
## 14: 0.005240502 -0.3857226 0.2263551 0.4554380
## 15: 0.005240502 -0.3857226 0.2263551 0.4554380
## 16: 0.005240502 -0.3857226 0.2263551 0.4554380
## 17: 0.005240502 -0.3857226 0.2263551 0.4554380
## 18: 0.005240502 -0.3857226 0.2263551 0.4554380
## 19: 0.005240502 -0.3857226 0.2263551 0.4554380
## 20: 0.005240502 -0.3857226 0.2263551 0.4554380
## 21: 0.005240502 -0.3857226 0.2263551 0.4554380
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.004740574 -1.0188938 0.3891921 0.7676649
## 25: 0.004740574 -1.0188938 0.3891921 0.7676649
## 26: 0.004740574 -1.0188938 0.3891921 0.7676649
## 27: 0.004740574 -1.0188938 0.3891921 0.7676649
## 28: 0.004740574 -1.0188938 0.3891921 0.7676649
## 29: 0.004740574 -1.0188938 0.3891921 0.7676649
## 30: 0.004740574 -1.0188938 0.3891921 0.7676649
## 31: 0.004740574 -1.0188938 0.3891921 0.7676649
## 32: 0.004740574 -1.0188938 0.3891921 0.7676649
## 33: 0.004740574 -1.0188938 0.3891921 0.7676649
## 34: 0.004740574 -1.0188938 0.3891921 0.7676649
## 35: 0.004740574 -1.0188938 0.3891921 0.7676649
## 36: 0.004740574 -1.0188938 0.3891921 0.7676649
## 37: 0.004740574 -1.0188938 0.3891921 0.7676649
## 38: 0.005096736 -0.1004869 0.4195148 0.9429681
## 39: 0.005096736 -0.1004869 0.4195148 0.9429681
## 40: 0.005096736 -0.1004869 0.4195148 0.9429681
## 41: 0.005096736 -0.1004869 0.4195148 0.9429681
## 42: 0.005096736 -0.1004869 0.4195148 0.9429681
## 43: 0.005096736 -0.1004869 0.4195148 0.9429681
## 44: 0.004909730 -1.3643003 0.7964977 0.0290061
## 45: 0.004909730 -1.3643003 0.7964977 0.0290061
## 46: 0.004909730 -1.3643003 0.7964977 0.0290061
## 47: 0.004909730 -1.3643003 0.7964977 0.0290061
## 48: 0.004909730 -1.3643003 0.7964977 0.0290061
## 49: 0.004909730 -1.3643003 0.7964977 0.0290061
## 50: 0.004909730 -1.3643003 0.7964977 0.0290061
## 51: 0.004909730 -1.3643003 0.7964977 0.0290061
## 52: 0.004909730 -1.3643003 0.7964977 0.0290061
## 53: 0.004909730 -1.3643003 0.7964977 0.0290061
## 54: 0.004909730 -1.3643003 0.7964977 0.0290061
## 55: 0.004909730 -1.3643003 0.7964977 0.0290061
## 56: 0.004909730 -1.3643003 0.7964977 0.0290061
## 57: 0.004909730 -1.3643003 0.7964977 0.0290061
## 58: 0.004909730 -1.3643003 0.7964977 0.0290061
## 59: 0.004909730 -1.3643003 0.7964977 0.0290061
## 60: 0.004107492 -1.6060807 0.6281863 0.3548128
## 61: 0.004107492 -1.6060807 0.6281863 0.3548128
## 62: 0.004107492 -1.6060807 0.6281863 0.3548128
## 63: 0.004107492 -1.6060807 0.6281863 0.3548128
## 64: 0.004107492 -1.6060807 0.6281863 0.3548128
## 65: 0.004107492 -1.6060807 0.6281863 0.3548128
## 66: 0.004107492 -1.6060807 0.6281863 0.3548128
## 67: 0.004107492 -1.6060807 0.6281863 0.3548128
## 68: 0.004107492 -1.6060807 0.6281863 0.3548128
## 69: 0.004107492 -1.6060807 0.6281863 0.3548128
## 70: 0.004107492 -1.6060807 0.6281863 0.3548128
## 71: 0.004107492 -1.6060807 0.6281863 0.3548128
## 72: 0.004107492 -1.6060807 0.6281863 0.3548128
## 73: 0.004107492 -1.6060807 0.6281863 0.3548128
## 74: 0.004107492 -1.6060807 0.6281863 0.3548128
## 75: 0.004107492 -1.6060807 0.6281863 0.3548128
## 76: 0.004107492 -1.6060807 0.6281863 0.3548128
## se.bp v c pchi
## [1] "ORF32" "ORF74" "ORF75" "ORF28" "ORF24" "ORF76" "ORF37" "ORF25" "ORF14"## [1] 9## [1] "ORF1" "ORF4" "ORF7" "ORF9" "ORF17" "ORF18" "ORF20"
## [8] "ORF21" "ORF24" "ORF28" "ORF31" "ORF32" "ORF34" "ORF38"
## [15] "ORF50" "ORF61" "ORF64_1" "ORF67_1" "ORF74" "ORF75" "NOIR_2"
## [22] "ORF2" "ORF3" "ORF8" "ORF11" "ORF19" "ORF22" "ORF26"
## [29] "ORF29" "ORF36" "ORF37" "CTO" "ORF40" "ORF51" "ORF66_1"
## [36] "ORF73" "ORF76" "ORF5" "ORF30" "ORF53" "ORF63" "ORF65_1"
## [43] "ORF69"## [1] 43Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 2: 1 ORF4 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 3: 1 ORF7 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 4: 1 ORF9 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 5: 1 ORF17 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 6: 1 ORF18 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 7: 1 ORF20 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 8: 1 ORF21 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 9: 1 ORF24 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 10: 1 ORF28 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 11: 1 ORF31 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 12: 1 ORF32 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 13: 1 ORF34 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 14: 1 ORF38 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 15: 1 ORF50 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 16: 1 ORF61 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 17: 1 ORF64_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 18: 1 ORF67_1 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 19: 1 ORF74 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 20: 1 ORF75 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 21: 1 NOIR_2 0.3416132 0.7297568 0.5633103 0.039627465 0.025401648
## 22: 2 ORF2 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 23: 2 ORF3 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 24: 2 ORF8 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 25: 2 ORF11 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 26: 2 ORF19 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 27: 2 ORF22 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 28: 2 ORF26 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 29: 2 ORF29 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 30: 2 ORF36 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 31: 2 ORF37 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 32: 2 CTO 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 33: 2 ORF40 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 34: 2 ORF51 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 35: 2 ORF66_1 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 36: 2 ORF73 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 37: 2 ORF76 0.7717718 0.9204472 0.7355551 0.025365875 0.011983718
## 38: 3 ORF5 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 39: 3 ORF30 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 40: 3 ORF53 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 41: 3 ORF63 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 42: 3 ORF65_1 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 43: 3 ORF69 0.1063624 0.6984688 0.3748527 0.045883461 0.027471846
## 44: 4 ORF6 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 45: 4 ORF13 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 46: 4 ORF15 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 47: 4 ORF16 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 48: 4 ORF33 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 49: 4 ORF42 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 50: 4 ORF52 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 51: 4 ORF54 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 52: 4 ORF60 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 53: 4 ORF72 0.9278650 0.9846445 0.7149155 0.011051205 0.003132839
## 54: 5 ORF10 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 55: 5 ORF12 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 56: 5 ORF14 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 57: 5 ORF23 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 58: 5 ORF27 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 59: 5 ORF35 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 60: 5 ORF39 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 61: 5 ORF41 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 62: 5 ORF44 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 63: 5 ORF48 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 64: 5 ORF49 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 65: 5 ORF57 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 66: 5 ORF59 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 67: 5 NOIR_1 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 68: 5 ORF68 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 69: 5 ORF70 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 70: 5 ORF71 0.9519412 0.9872672 0.8359367 0.008610418 0.002908120
## 71: 6 ORF25 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 72: 6 ORF35.5 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 73: 6 ORF43 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 74: 6 ORF46 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 75: 6 ORF58 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## 76: 6 ORF62 0.6890515 0.8780627 0.7316787 0.030387484 0.016370972
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.005240502 -0.3857226 0.2263551 0.4554380
## 2: 0.005240502 -0.3857226 0.2263551 0.4554380
## 3: 0.005240502 -0.3857226 0.2263551 0.4554380
## 4: 0.005240502 -0.3857226 0.2263551 0.4554380
## 5: 0.005240502 -0.3857226 0.2263551 0.4554380
## 6: 0.005240502 -0.3857226 0.2263551 0.4554380
## 7: 0.005240502 -0.3857226 0.2263551 0.4554380
## 8: 0.005240502 -0.3857226 0.2263551 0.4554380
## 9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.005240502 -0.3857226 0.2263551 0.4554380
## 14: 0.005240502 -0.3857226 0.2263551 0.4554380
## 15: 0.005240502 -0.3857226 0.2263551 0.4554380
## 16: 0.005240502 -0.3857226 0.2263551 0.4554380
## 17: 0.005240502 -0.3857226 0.2263551 0.4554380
## 18: 0.005240502 -0.3857226 0.2263551 0.4554380
## 19: 0.005240502 -0.3857226 0.2263551 0.4554380
## 20: 0.005240502 -0.3857226 0.2263551 0.4554380
## 21: 0.005240502 -0.3857226 0.2263551 0.4554380
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.004740574 -1.0188938 0.3891921 0.7676649
## 25: 0.004740574 -1.0188938 0.3891921 0.7676649
## 26: 0.004740574 -1.0188938 0.3891921 0.7676649
## 27: 0.004740574 -1.0188938 0.3891921 0.7676649
## 28: 0.004740574 -1.0188938 0.3891921 0.7676649
## 29: 0.004740574 -1.0188938 0.3891921 0.7676649
## 30: 0.004740574 -1.0188938 0.3891921 0.7676649
## 31: 0.004740574 -1.0188938 0.3891921 0.7676649
## 32: 0.004740574 -1.0188938 0.3891921 0.7676649
## 33: 0.004740574 -1.0188938 0.3891921 0.7676649
## 34: 0.004740574 -1.0188938 0.3891921 0.7676649
## 35: 0.004740574 -1.0188938 0.3891921 0.7676649
## 36: 0.004740574 -1.0188938 0.3891921 0.7676649
## 37: 0.004740574 -1.0188938 0.3891921 0.7676649
## 38: 0.005096736 -0.1004869 0.4195148 0.9429681
## 39: 0.005096736 -0.1004869 0.4195148 0.9429681
## 40: 0.005096736 -0.1004869 0.4195148 0.9429681
## 41: 0.005096736 -0.1004869 0.4195148 0.9429681
## 42: 0.005096736 -0.1004869 0.4195148 0.9429681
## 43: 0.005096736 -0.1004869 0.4195148 0.9429681
## 44: 0.004909730 -1.3643003 0.7964977 0.0290061
## 45: 0.004909730 -1.3643003 0.7964977 0.0290061
## 46: 0.004909730 -1.3643003 0.7964977 0.0290061
## 47: 0.004909730 -1.3643003 0.7964977 0.0290061
## 48: 0.004909730 -1.3643003 0.7964977 0.0290061
## 49: 0.004909730 -1.3643003 0.7964977 0.0290061
## 50: 0.004909730 -1.3643003 0.7964977 0.0290061
## 51: 0.004909730 -1.3643003 0.7964977 0.0290061
## 52: 0.004909730 -1.3643003 0.7964977 0.0290061
## 53: 0.004909730 -1.3643003 0.7964977 0.0290061
## 54: 0.004107492 -1.6060807 0.6281863 0.3548128
## 55: 0.004107492 -1.6060807 0.6281863 0.3548128
## 56: 0.004107492 -1.6060807 0.6281863 0.3548128
## 57: 0.004107492 -1.6060807 0.6281863 0.3548128
## 58: 0.004107492 -1.6060807 0.6281863 0.3548128
## 59: 0.004107492 -1.6060807 0.6281863 0.3548128
## 60: 0.004107492 -1.6060807 0.6281863 0.3548128
## 61: 0.004107492 -1.6060807 0.6281863 0.3548128
## 62: 0.004107492 -1.6060807 0.6281863 0.3548128
## 63: 0.004107492 -1.6060807 0.6281863 0.3548128
## 64: 0.004107492 -1.6060807 0.6281863 0.3548128
## 65: 0.004107492 -1.6060807 0.6281863 0.3548128
## 66: 0.004107492 -1.6060807 0.6281863 0.3548128
## 67: 0.004107492 -1.6060807 0.6281863 0.3548128
## 68: 0.004107492 -1.6060807 0.6281863 0.3548128
## 69: 0.004107492 -1.6060807 0.6281863 0.3548128
## 70: 0.004107492 -1.6060807 0.6281863 0.3548128
## 71: 0.004747012 -0.8916273 0.2737294 0.4292636
## 72: 0.004747012 -0.8916273 0.2737294 0.4292636
## 73: 0.004747012 -0.8916273 0.2737294 0.4292636
## 74: 0.004747012 -0.8916273 0.2737294 0.4292636
## 75: 0.004747012 -0.8916273 0.2737294 0.4292636
## 76: 0.004747012 -0.8916273 0.2737294 0.4292636
## se.bp v c pchi
## [1] "ORF32" "ORF74" "ORF75" "ORF28" "ORF24" "ORF73" "ORF8" "CTO" "ORF76"
## [10] "ORF22" "ORF37" "ORF42" "ORF33" "ORF23" "ORF14"## [1] 15## [1] "ORF1" "ORF4" "ORF7" "ORF9" "ORF17" "ORF18" "ORF20"
## [8] "ORF21" "ORF24" "ORF28" "ORF31" "ORF32" "ORF34" "ORF38"
## [15] "ORF50" "ORF61" "ORF64_1" "ORF67_1" "ORF74" "ORF75" "NOIR_2"
## [22] "ORF2" "ORF3" "ORF8" "ORF11" "ORF19" "ORF22" "ORF26"
## [29] "ORF29" "ORF36" "ORF37" "CTO" "ORF40" "ORF51" "ORF66_1"
## [36] "ORF73" "ORF76" "ORF5" "ORF30" "ORF53" "ORF63" "ORF65_1"
## [43] "ORF69" "ORF25" "ORF35.5" "ORF43" "ORF46" "ORF58" "ORF62"## [1] 49Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 2: 1 ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 3: 1 ORF7 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 4: 1 ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 5: 1 ORF17 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 6: 1 ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 7: 1 ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 8: 1 ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 9: 1 ORF24 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10: 1 ORF28 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11: 1 ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12: 1 ORF32 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13: 1 ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 14: 1 ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 15: 1 ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 16: 1 ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 17: 1 ORF64_1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 18: 1 ORF67_1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 19: 1 ORF74 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 20: 1 ORF75 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 21: 1 NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 22: 2 ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23: 2 ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24: 2 ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 25: 2 ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 26: 2 ORF19 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 27: 2 ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 28: 2 ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 29: 2 ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 30: 2 ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 31: 2 ORF37 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 32: 2 CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 33: 2 ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 34: 2 ORF51 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 35: 2 ORF66_1 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 36: 2 ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 37: 2 ORF76 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 38: 3 ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 39: 3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 40: 3 ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 41: 4 ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 42: 4 ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 43: 4 ORF15 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 44: 4 ORF16 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 45: 4 ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 46: 4 ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 47: 4 ORF52 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 48: 4 ORF54 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 49: 4 ORF60 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 50: 4 ORF72 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 51: 5 ORF10 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 52: 5 ORF12 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 53: 5 ORF14 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 54: 5 ORF23 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 55: 5 ORF27 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 56: 5 ORF35 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 57: 5 ORF39 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 58: 5 ORF41 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 59: 5 ORF44 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 60: 5 ORF48 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 61: 5 ORF49 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 62: 5 ORF57 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 63: 5 ORF59 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 64: 5 NOIR_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 65: 5 ORF68 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 66: 5 ORF70 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 67: 5 ORF71 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 68: 6 ORF25 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 69: 6 ORF35.5 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 70: 6 ORF43 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 71: 6 ORF46 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 72: 6 ORF58 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 73: 6 ORF62 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 74: 7 ORF30 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 75: 7 ORF53 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 76: 7 ORF63 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.005240502 -0.3857226 0.2263551 0.4554380
## 2: 0.005240502 -0.3857226 0.2263551 0.4554380
## 3: 0.005240502 -0.3857226 0.2263551 0.4554380
## 4: 0.005240502 -0.3857226 0.2263551 0.4554380
## 5: 0.005240502 -0.3857226 0.2263551 0.4554380
## 6: 0.005240502 -0.3857226 0.2263551 0.4554380
## 7: 0.005240502 -0.3857226 0.2263551 0.4554380
## 8: 0.005240502 -0.3857226 0.2263551 0.4554380
## 9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.005240502 -0.3857226 0.2263551 0.4554380
## 14: 0.005240502 -0.3857226 0.2263551 0.4554380
## 15: 0.005240502 -0.3857226 0.2263551 0.4554380
## 16: 0.005240502 -0.3857226 0.2263551 0.4554380
## 17: 0.005240502 -0.3857226 0.2263551 0.4554380
## 18: 0.005240502 -0.3857226 0.2263551 0.4554380
## 19: 0.005240502 -0.3857226 0.2263551 0.4554380
## 20: 0.005240502 -0.3857226 0.2263551 0.4554380
## 21: 0.005240502 -0.3857226 0.2263551 0.4554380
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.004740574 -1.0188938 0.3891921 0.7676649
## 25: 0.004740574 -1.0188938 0.3891921 0.7676649
## 26: 0.004740574 -1.0188938 0.3891921 0.7676649
## 27: 0.004740574 -1.0188938 0.3891921 0.7676649
## 28: 0.004740574 -1.0188938 0.3891921 0.7676649
## 29: 0.004740574 -1.0188938 0.3891921 0.7676649
## 30: 0.004740574 -1.0188938 0.3891921 0.7676649
## 31: 0.004740574 -1.0188938 0.3891921 0.7676649
## 32: 0.004740574 -1.0188938 0.3891921 0.7676649
## 33: 0.004740574 -1.0188938 0.3891921 0.7676649
## 34: 0.004740574 -1.0188938 0.3891921 0.7676649
## 35: 0.004740574 -1.0188938 0.3891921 0.7676649
## 36: 0.004740574 -1.0188938 0.3891921 0.7676649
## 37: 0.004740574 -1.0188938 0.3891921 0.7676649
## 38: 0.005096736 -0.1004869 0.4195148 0.9429681
## 39: 0.005096736 -0.1004869 0.4195148 0.9429681
## 40: 0.005096736 -0.1004869 0.4195148 0.9429681
## 41: 0.004909730 -1.3643003 0.7964977 0.0290061
## 42: 0.004909730 -1.3643003 0.7964977 0.0290061
## 43: 0.004909730 -1.3643003 0.7964977 0.0290061
## 44: 0.004909730 -1.3643003 0.7964977 0.0290061
## 45: 0.004909730 -1.3643003 0.7964977 0.0290061
## 46: 0.004909730 -1.3643003 0.7964977 0.0290061
## 47: 0.004909730 -1.3643003 0.7964977 0.0290061
## 48: 0.004909730 -1.3643003 0.7964977 0.0290061
## 49: 0.004909730 -1.3643003 0.7964977 0.0290061
## 50: 0.004909730 -1.3643003 0.7964977 0.0290061
## 51: 0.004107492 -1.6060807 0.6281863 0.3548128
## 52: 0.004107492 -1.6060807 0.6281863 0.3548128
## 53: 0.004107492 -1.6060807 0.6281863 0.3548128
## 54: 0.004107492 -1.6060807 0.6281863 0.3548128
## 55: 0.004107492 -1.6060807 0.6281863 0.3548128
## 56: 0.004107492 -1.6060807 0.6281863 0.3548128
## 57: 0.004107492 -1.6060807 0.6281863 0.3548128
## 58: 0.004107492 -1.6060807 0.6281863 0.3548128
## 59: 0.004107492 -1.6060807 0.6281863 0.3548128
## 60: 0.004107492 -1.6060807 0.6281863 0.3548128
## 61: 0.004107492 -1.6060807 0.6281863 0.3548128
## 62: 0.004107492 -1.6060807 0.6281863 0.3548128
## 63: 0.004107492 -1.6060807 0.6281863 0.3548128
## 64: 0.004107492 -1.6060807 0.6281863 0.3548128
## 65: 0.004107492 -1.6060807 0.6281863 0.3548128
## 66: 0.004107492 -1.6060807 0.6281863 0.3548128
## 67: 0.004107492 -1.6060807 0.6281863 0.3548128
## 68: 0.004747012 -0.8916273 0.2737294 0.4292636
## 69: 0.004747012 -0.8916273 0.2737294 0.4292636
## 70: 0.004747012 -0.8916273 0.2737294 0.4292636
## 71: 0.004747012 -0.8916273 0.2737294 0.4292636
## 72: 0.004747012 -0.8916273 0.2737294 0.4292636
## 73: 0.004747012 -0.8916273 0.2737294 0.4292636
## 74: 0.001974539 -2.6297796 0.6681400 0.6408455
## 75: 0.001974539 -2.6297796 0.6681400 0.6408455
## 76: 0.001974539 -2.6297796 0.6681400 0.6408455
## se.bp v c pchi
## [1] "ORF32" "ORF74" "ORF75" "ORF28" "ORF24" "ORF73" "ORF8" "CTO" "ORF76"
## [10] "ORF22" "ORF37" "ORF42" "ORF33" "ORF23" "ORF14" "ORF63"## [1] 16## [1] "ORF1" "ORF4" "ORF7" "ORF9" "ORF17" "ORF18" "ORF20"
## [8] "ORF21" "ORF24" "ORF28" "ORF31" "ORF32" "ORF34" "ORF38"
## [15] "ORF50" "ORF61" "ORF64_1" "ORF67_1" "ORF74" "ORF75" "NOIR_2"
## [22] "ORF2" "ORF3" "ORF8" "ORF11" "ORF19" "ORF22" "ORF26"
## [29] "ORF29" "ORF36" "ORF37" "CTO" "ORF40" "ORF51" "ORF66_1"
## [36] "ORF73" "ORF76" "ORF5" "ORF65_1" "ORF69" "ORF25" "ORF35.5"
## [43] "ORF43" "ORF46" "ORF58" "ORF62"## [1] 46Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 2: 1 ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 3: 1 ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 4: 1 ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 5: 1 ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 6: 1 ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 7: 1 ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 8: 1 ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 9: 1 ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10: 1 ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11: 1 ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12: 1 NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13: 2 ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 14: 2 ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 15: 2 ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 16: 2 ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 17: 2 ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 18: 2 ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 19: 2 ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 20: 2 ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 21: 2 CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 22: 2 ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23: 2 ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24: 3 ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 25: 3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 26: 3 ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 27: 4 ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 28: 4 ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 29: 4 ORF15 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 30: 4 ORF16 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 31: 4 ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 32: 4 ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 33: 4 ORF52 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 34: 4 ORF54 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 35: 4 ORF60 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 36: 4 ORF72 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 37: 5 ORF7 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 38: 5 ORF17 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 39: 5 ORF24 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 40: 5 ORF28 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 41: 5 ORF32 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 42: 5 ORF64_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 43: 5 ORF67_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 44: 5 ORF74 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 45: 5 ORF75 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 46: 6 ORF10 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 47: 7 ORF12 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 48: 7 ORF14 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 49: 7 ORF23 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 50: 7 ORF27 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 51: 7 ORF35 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 52: 7 ORF39 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 53: 7 ORF41 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 54: 7 ORF44 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 55: 7 ORF48 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 56: 7 ORF49 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 57: 7 ORF57 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 58: 7 ORF59 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 59: 7 NOIR_1 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 60: 7 ORF68 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 61: 7 ORF70 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 62: 7 ORF71 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 63: 8 ORF19 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 64: 8 ORF37 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 65: 8 ORF51 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 66: 8 ORF66_1 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 67: 8 ORF76 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 68: 9 ORF25 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 69: 9 ORF35.5 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 70: 9 ORF43 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 71: 9 ORF46 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 72: 9 ORF58 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 73: 9 ORF62 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 74: 10 ORF30 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 75: 10 ORF53 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 76: 10 ORF63 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.005240502 -0.3857226 0.2263551 0.4554380
## 2: 0.005240502 -0.3857226 0.2263551 0.4554380
## 3: 0.005240502 -0.3857226 0.2263551 0.4554380
## 4: 0.005240502 -0.3857226 0.2263551 0.4554380
## 5: 0.005240502 -0.3857226 0.2263551 0.4554380
## 6: 0.005240502 -0.3857226 0.2263551 0.4554380
## 7: 0.005240502 -0.3857226 0.2263551 0.4554380
## 8: 0.005240502 -0.3857226 0.2263551 0.4554380
## 9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.004740574 -1.0188938 0.3891921 0.7676649
## 14: 0.004740574 -1.0188938 0.3891921 0.7676649
## 15: 0.004740574 -1.0188938 0.3891921 0.7676649
## 16: 0.004740574 -1.0188938 0.3891921 0.7676649
## 17: 0.004740574 -1.0188938 0.3891921 0.7676649
## 18: 0.004740574 -1.0188938 0.3891921 0.7676649
## 19: 0.004740574 -1.0188938 0.3891921 0.7676649
## 20: 0.004740574 -1.0188938 0.3891921 0.7676649
## 21: 0.004740574 -1.0188938 0.3891921 0.7676649
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.005096736 -0.1004869 0.4195148 0.9429681
## 25: 0.005096736 -0.1004869 0.4195148 0.9429681
## 26: 0.005096736 -0.1004869 0.4195148 0.9429681
## 27: 0.004909730 -1.3643003 0.7964977 0.0290061
## 28: 0.004909730 -1.3643003 0.7964977 0.0290061
## 29: 0.004909730 -1.3643003 0.7964977 0.0290061
## 30: 0.004909730 -1.3643003 0.7964977 0.0290061
## 31: 0.004909730 -1.3643003 0.7964977 0.0290061
## 32: 0.004909730 -1.3643003 0.7964977 0.0290061
## 33: 0.004909730 -1.3643003 0.7964977 0.0290061
## 34: 0.004909730 -1.3643003 0.7964977 0.0290061
## 35: 0.004909730 -1.3643003 0.7964977 0.0290061
## 36: 0.004909730 -1.3643003 0.7964977 0.0290061
## 37: 0.004107492 -1.6060807 0.6281863 0.3548128
## 38: 0.004107492 -1.6060807 0.6281863 0.3548128
## 39: 0.004107492 -1.6060807 0.6281863 0.3548128
## 40: 0.004107492 -1.6060807 0.6281863 0.3548128
## 41: 0.004107492 -1.6060807 0.6281863 0.3548128
## 42: 0.004107492 -1.6060807 0.6281863 0.3548128
## 43: 0.004107492 -1.6060807 0.6281863 0.3548128
## 44: 0.004107492 -1.6060807 0.6281863 0.3548128
## 45: 0.004107492 -1.6060807 0.6281863 0.3548128
## 46: 0.004747012 -0.8916273 0.2737294 0.4292636
## 47: 0.001974539 -2.6297796 0.6681400 0.6408455
## 48: 0.001974539 -2.6297796 0.6681400 0.6408455
## 49: 0.001974539 -2.6297796 0.6681400 0.6408455
## 50: 0.001974539 -2.6297796 0.6681400 0.6408455
## 51: 0.001974539 -2.6297796 0.6681400 0.6408455
## 52: 0.001974539 -2.6297796 0.6681400 0.6408455
## 53: 0.001974539 -2.6297796 0.6681400 0.6408455
## 54: 0.001974539 -2.6297796 0.6681400 0.6408455
## 55: 0.001974539 -2.6297796 0.6681400 0.6408455
## 56: 0.001974539 -2.6297796 0.6681400 0.6408455
## 57: 0.001974539 -2.6297796 0.6681400 0.6408455
## 58: 0.001974539 -2.6297796 0.6681400 0.6408455
## 59: 0.001974539 -2.6297796 0.6681400 0.6408455
## 60: 0.001974539 -2.6297796 0.6681400 0.6408455
## 61: 0.001974539 -2.6297796 0.6681400 0.6408455
## 62: 0.001974539 -2.6297796 0.6681400 0.6408455
## 63: 0.003927220 -1.7307215 0.6541499 0.4863678
## 64: 0.003927220 -1.7307215 0.6541499 0.4863678
## 65: 0.003927220 -1.7307215 0.6541499 0.4863678
## 66: 0.003927220 -1.7307215 0.6541499 0.4863678
## 67: 0.003927220 -1.7307215 0.6541499 0.4863678
## 68: 0.004045947 -1.1019554 0.1437770 0.6282165
## 69: 0.004045947 -1.1019554 0.1437770 0.6282165
## 70: 0.004045947 -1.1019554 0.1437770 0.6282165
## 71: 0.004045947 -1.1019554 0.1437770 0.6282165
## 72: 0.004045947 -1.1019554 0.1437770 0.6282165
## 73: 0.004045947 -1.1019554 0.1437770 0.6282165
## 74: 0.005256888 -0.8090952 0.6096982 0.4091181
## 75: 0.005256888 -0.8090952 0.6096982 0.4091181
## 76: 0.005256888 -0.8090952 0.6096982 0.4091181
## se.bp v c pchi
## [1] "ORF42" "ORF33" "ORF67_1" "ORF39" "ORF23" "ORF35" "NOIR_1"
## [8] "ORF14" "ORF76" "ORF63"## [1] 10## [1] "ORF1" "ORF4" "ORF9" "ORF18" "ORF20" "ORF21" "ORF31"
## [8] "ORF34" "ORF38" "ORF50" "ORF61" "NOIR_2" "ORF2" "ORF3"
## [15] "ORF8" "ORF11" "ORF22" "ORF26" "ORF29" "ORF36" "CTO"
## [22] "ORF40" "ORF73" "ORF5" "ORF65_1" "ORF69" "ORF10" "ORF25"
## [29] "ORF35.5" "ORF43" "ORF46" "ORF58" "ORF62" "ORF30" "ORF53"
## [36] "ORF63"## [1] 36Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 2: 1 ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 3: 1 ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 4: 1 ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 5: 1 ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 6: 1 ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 7: 1 ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 8: 1 ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 9: 1 ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10: 1 ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11: 1 ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12: 1 NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13: 2 ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 14: 2 ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 15: 2 ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 16: 2 ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 17: 2 ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 18: 2 ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 19: 2 ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 20: 2 ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 21: 2 CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 22: 2 ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23: 2 ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24: 3 ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 25: 3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 26: 3 ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 27: 4 ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 28: 4 ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 29: 4 ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 30: 4 ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 31: 5 ORF7 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 32: 5 ORF17 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 33: 5 ORF24 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 34: 5 ORF28 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 35: 5 ORF32 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 36: 5 ORF64_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 37: 5 ORF67_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 38: 5 ORF74 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 39: 5 ORF75 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 40: 6 ORF10 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 41: 7 ORF12 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 42: 7 ORF27 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 43: 7 ORF35 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 44: 7 ORF41 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 45: 7 ORF44 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 46: 7 ORF49 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 47: 7 ORF59 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 48: 7 NOIR_1 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 49: 7 ORF70 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 50: 8 ORF14 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 51: 8 ORF23 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 52: 8 ORF39 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 53: 8 ORF48 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 54: 8 ORF57 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 55: 8 ORF68 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 56: 8 ORF71 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 57: 9 ORF15 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 58: 9 ORF16 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 59: 9 ORF52 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 60: 9 ORF54 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 61: 9 ORF60 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 62: 9 ORF72 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 63: 10 ORF19 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 64: 10 ORF37 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 65: 10 ORF51 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 66: 10 ORF66_1 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 67: 10 ORF76 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 68: 11 ORF25 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 69: 11 ORF35.5 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 70: 11 ORF43 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 71: 11 ORF46 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 72: 11 ORF58 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 73: 11 ORF62 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 74: 12 ORF30 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 75: 12 ORF53 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 76: 12 ORF63 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.005240502 -0.3857226 0.2263551 0.4554380
## 2: 0.005240502 -0.3857226 0.2263551 0.4554380
## 3: 0.005240502 -0.3857226 0.2263551 0.4554380
## 4: 0.005240502 -0.3857226 0.2263551 0.4554380
## 5: 0.005240502 -0.3857226 0.2263551 0.4554380
## 6: 0.005240502 -0.3857226 0.2263551 0.4554380
## 7: 0.005240502 -0.3857226 0.2263551 0.4554380
## 8: 0.005240502 -0.3857226 0.2263551 0.4554380
## 9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.004740574 -1.0188938 0.3891921 0.7676649
## 14: 0.004740574 -1.0188938 0.3891921 0.7676649
## 15: 0.004740574 -1.0188938 0.3891921 0.7676649
## 16: 0.004740574 -1.0188938 0.3891921 0.7676649
## 17: 0.004740574 -1.0188938 0.3891921 0.7676649
## 18: 0.004740574 -1.0188938 0.3891921 0.7676649
## 19: 0.004740574 -1.0188938 0.3891921 0.7676649
## 20: 0.004740574 -1.0188938 0.3891921 0.7676649
## 21: 0.004740574 -1.0188938 0.3891921 0.7676649
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.005096736 -0.1004869 0.4195148 0.9429681
## 25: 0.005096736 -0.1004869 0.4195148 0.9429681
## 26: 0.005096736 -0.1004869 0.4195148 0.9429681
## 27: 0.004909730 -1.3643003 0.7964977 0.0290061
## 28: 0.004909730 -1.3643003 0.7964977 0.0290061
## 29: 0.004909730 -1.3643003 0.7964977 0.0290061
## 30: 0.004909730 -1.3643003 0.7964977 0.0290061
## 31: 0.004107492 -1.6060807 0.6281863 0.3548128
## 32: 0.004107492 -1.6060807 0.6281863 0.3548128
## 33: 0.004107492 -1.6060807 0.6281863 0.3548128
## 34: 0.004107492 -1.6060807 0.6281863 0.3548128
## 35: 0.004107492 -1.6060807 0.6281863 0.3548128
## 36: 0.004107492 -1.6060807 0.6281863 0.3548128
## 37: 0.004107492 -1.6060807 0.6281863 0.3548128
## 38: 0.004107492 -1.6060807 0.6281863 0.3548128
## 39: 0.004107492 -1.6060807 0.6281863 0.3548128
## 40: 0.004747012 -0.8916273 0.2737294 0.4292636
## 41: 0.001974539 -2.6297796 0.6681400 0.6408455
## 42: 0.001974539 -2.6297796 0.6681400 0.6408455
## 43: 0.001974539 -2.6297796 0.6681400 0.6408455
## 44: 0.001974539 -2.6297796 0.6681400 0.6408455
## 45: 0.001974539 -2.6297796 0.6681400 0.6408455
## 46: 0.001974539 -2.6297796 0.6681400 0.6408455
## 47: 0.001974539 -2.6297796 0.6681400 0.6408455
## 48: 0.001974539 -2.6297796 0.6681400 0.6408455
## 49: 0.001974539 -2.6297796 0.6681400 0.6408455
## 50: 0.003927220 -1.7307215 0.6541499 0.4863678
## 51: 0.003927220 -1.7307215 0.6541499 0.4863678
## 52: 0.003927220 -1.7307215 0.6541499 0.4863678
## 53: 0.003927220 -1.7307215 0.6541499 0.4863678
## 54: 0.003927220 -1.7307215 0.6541499 0.4863678
## 55: 0.003927220 -1.7307215 0.6541499 0.4863678
## 56: 0.003927220 -1.7307215 0.6541499 0.4863678
## 57: 0.004045947 -1.1019554 0.1437770 0.6282165
## 58: 0.004045947 -1.1019554 0.1437770 0.6282165
## 59: 0.004045947 -1.1019554 0.1437770 0.6282165
## 60: 0.004045947 -1.1019554 0.1437770 0.6282165
## 61: 0.004045947 -1.1019554 0.1437770 0.6282165
## 62: 0.004045947 -1.1019554 0.1437770 0.6282165
## 63: 0.005256888 -0.8090952 0.6096982 0.4091181
## 64: 0.005256888 -0.8090952 0.6096982 0.4091181
## 65: 0.005256888 -0.8090952 0.6096982 0.4091181
## 66: 0.005256888 -0.8090952 0.6096982 0.4091181
## 67: 0.005256888 -0.8090952 0.6096982 0.4091181
## 68: 0.003699662 -1.7457057 0.5965758 0.2636889
## 69: 0.003699662 -1.7457057 0.5965758 0.2636889
## 70: 0.003699662 -1.7457057 0.5965758 0.2636889
## 71: 0.003699662 -1.7457057 0.5965758 0.2636889
## 72: 0.003699662 -1.7457057 0.5965758 0.2636889
## 73: 0.003699662 -1.7457057 0.5965758 0.2636889
## 74: 0.003612836 -1.5562853 0.3815687 0.4734673
## 75: 0.003612836 -1.5562853 0.3815687 0.4734673
## 76: 0.003612836 -1.5562853 0.3815687 0.4734673
## se.bp v c pchi
## [1] "ORF75" "ORF32" "ORF67_1" "ORF28" "ORF24" "ORF14" "ORF57"
## [8] "ORF76" "ORF62" "ORF63"## [1] 10## [1] "ORF1" "ORF4" "ORF9" "ORF18" "ORF20" "ORF21" "ORF31"
## [8] "ORF34" "ORF38" "ORF50" "ORF61" "NOIR_2" "ORF2" "ORF3"
## [15] "ORF8" "ORF11" "ORF22" "ORF26" "ORF29" "ORF36" "CTO"
## [22] "ORF40" "ORF73" "ORF5" "ORF65_1" "ORF69" "ORF10" "ORF15"
## [29] "ORF16" "ORF52" "ORF54" "ORF60" "ORF72" "ORF19" "ORF37"
## [36] "ORF51" "ORF66_1" "ORF76"## [1] 38Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 2: 1 ORF4 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 3: 1 ORF9 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 4: 1 ORF18 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 5: 1 ORF20 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 6: 1 ORF21 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 7: 1 ORF31 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 8: 1 ORF34 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 9: 1 ORF38 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 10: 1 ORF50 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 11: 1 ORF61 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 12: 1 NOIR_2 0.3416132 0.7297568 0.5633103 0.0396274647 0.0254016483
## 13: 2 ORF2 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 14: 2 ORF3 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 15: 2 ORF8 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 16: 2 ORF11 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 17: 2 ORF22 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 18: 2 ORF26 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 19: 2 ORF29 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 20: 2 ORF36 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 21: 2 CTO 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 22: 2 ORF40 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 23: 2 ORF73 0.7717718 0.9204472 0.7355551 0.0253658752 0.0119837178
## 24: 3 ORF5 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 25: 3 ORF65_1 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 26: 3 ORF69 0.1063624 0.6984688 0.3748527 0.0458834611 0.0274718458
## 27: 4 ORF6 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 28: 4 ORF13 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 29: 4 ORF33 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 30: 4 ORF42 0.9278650 0.9846445 0.7149155 0.0110512047 0.0031328392
## 31: 5 ORF7 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 32: 5 ORF17 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 33: 5 ORF24 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 34: 5 ORF28 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 35: 5 ORF32 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 36: 5 ORF64_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 37: 5 ORF67_1 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 38: 5 ORF74 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 39: 5 ORF75 0.9519412 0.9872672 0.8359367 0.0086104181 0.0029081196
## 40: 6 ORF10 0.6890515 0.8780627 0.7316787 0.0303874839 0.0163709722
## 41: 7 ORF12 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 42: 7 ORF27 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 43: 7 ORF35 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 44: 7 ORF41 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 45: 7 ORF44 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 46: 7 ORF49 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 47: 7 ORF59 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 48: 7 NOIR_1 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 49: 7 ORF70 0.9980676 0.9995130 0.9750978 0.0008952628 0.0002644737
## 50: 8 ORF14 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 51: 8 ORF23 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 52: 8 ORF39 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 53: 8 ORF48 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 54: 8 ORF57 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 55: 8 ORF68 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 56: 8 ORF71 0.9666967 0.9914575 0.8591642 0.0066450669 0.0021473415
## 57: 9 ORF15 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 58: 9 ORF16 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 59: 9 ORF52 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 60: 9 ORF54 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 61: 9 ORF60 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 62: 9 ORF72 0.7596610 0.8935687 0.8310136 0.0277895980 0.0161101830
## 63: 10 ORF19 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 64: 10 ORF37 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 65: 10 ORF51 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 66: 10 ORF66_1 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 67: 10 ORF76 0.7122851 0.9220204 0.5790239 0.0291256744 0.0113429227
## 68: 11 ORF25 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 69: 11 ORF35.5 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 70: 11 ORF43 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 71: 11 ORF46 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 72: 11 ORF58 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 73: 11 ORF62 0.9652023 0.9904169 0.8747488 0.0069338476 0.0023925448
## 74: 12 ORF30 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 75: 12 ORF53 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## 76: 12 ORF63 0.9250961 0.9736795 0.8799459 0.0131254949 0.0057945709
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.005240502 -0.3857226 0.2263551 0.4554380
## 2: 0.005240502 -0.3857226 0.2263551 0.4554380
## 3: 0.005240502 -0.3857226 0.2263551 0.4554380
## 4: 0.005240502 -0.3857226 0.2263551 0.4554380
## 5: 0.005240502 -0.3857226 0.2263551 0.4554380
## 6: 0.005240502 -0.3857226 0.2263551 0.4554380
## 7: 0.005240502 -0.3857226 0.2263551 0.4554380
## 8: 0.005240502 -0.3857226 0.2263551 0.4554380
## 9: 0.005240502 -0.3857226 0.2263551 0.4554380
## 10: 0.005240502 -0.3857226 0.2263551 0.4554380
## 11: 0.005240502 -0.3857226 0.2263551 0.4554380
## 12: 0.005240502 -0.3857226 0.2263551 0.4554380
## 13: 0.004740574 -1.0188938 0.3891921 0.7676649
## 14: 0.004740574 -1.0188938 0.3891921 0.7676649
## 15: 0.004740574 -1.0188938 0.3891921 0.7676649
## 16: 0.004740574 -1.0188938 0.3891921 0.7676649
## 17: 0.004740574 -1.0188938 0.3891921 0.7676649
## 18: 0.004740574 -1.0188938 0.3891921 0.7676649
## 19: 0.004740574 -1.0188938 0.3891921 0.7676649
## 20: 0.004740574 -1.0188938 0.3891921 0.7676649
## 21: 0.004740574 -1.0188938 0.3891921 0.7676649
## 22: 0.004740574 -1.0188938 0.3891921 0.7676649
## 23: 0.004740574 -1.0188938 0.3891921 0.7676649
## 24: 0.005096736 -0.1004869 0.4195148 0.9429681
## 25: 0.005096736 -0.1004869 0.4195148 0.9429681
## 26: 0.005096736 -0.1004869 0.4195148 0.9429681
## 27: 0.004909730 -1.3643003 0.7964977 0.0290061
## 28: 0.004909730 -1.3643003 0.7964977 0.0290061
## 29: 0.004909730 -1.3643003 0.7964977 0.0290061
## 30: 0.004909730 -1.3643003 0.7964977 0.0290061
## 31: 0.004107492 -1.6060807 0.6281863 0.3548128
## 32: 0.004107492 -1.6060807 0.6281863 0.3548128
## 33: 0.004107492 -1.6060807 0.6281863 0.3548128
## 34: 0.004107492 -1.6060807 0.6281863 0.3548128
## 35: 0.004107492 -1.6060807 0.6281863 0.3548128
## 36: 0.004107492 -1.6060807 0.6281863 0.3548128
## 37: 0.004107492 -1.6060807 0.6281863 0.3548128
## 38: 0.004107492 -1.6060807 0.6281863 0.3548128
## 39: 0.004107492 -1.6060807 0.6281863 0.3548128
## 40: 0.004747012 -0.8916273 0.2737294 0.4292636
## 41: 0.001974539 -2.6297796 0.6681400 0.6408455
## 42: 0.001974539 -2.6297796 0.6681400 0.6408455
## 43: 0.001974539 -2.6297796 0.6681400 0.6408455
## 44: 0.001974539 -2.6297796 0.6681400 0.6408455
## 45: 0.001974539 -2.6297796 0.6681400 0.6408455
## 46: 0.001974539 -2.6297796 0.6681400 0.6408455
## 47: 0.001974539 -2.6297796 0.6681400 0.6408455
## 48: 0.001974539 -2.6297796 0.6681400 0.6408455
## 49: 0.001974539 -2.6297796 0.6681400 0.6408455
## 50: 0.003927220 -1.7307215 0.6541499 0.4863678
## 51: 0.003927220 -1.7307215 0.6541499 0.4863678
## 52: 0.003927220 -1.7307215 0.6541499 0.4863678
## 53: 0.003927220 -1.7307215 0.6541499 0.4863678
## 54: 0.003927220 -1.7307215 0.6541499 0.4863678
## 55: 0.003927220 -1.7307215 0.6541499 0.4863678
## 56: 0.003927220 -1.7307215 0.6541499 0.4863678
## 57: 0.004045947 -1.1019554 0.1437770 0.6282165
## 58: 0.004045947 -1.1019554 0.1437770 0.6282165
## 59: 0.004045947 -1.1019554 0.1437770 0.6282165
## 60: 0.004045947 -1.1019554 0.1437770 0.6282165
## 61: 0.004045947 -1.1019554 0.1437770 0.6282165
## 62: 0.004045947 -1.1019554 0.1437770 0.6282165
## 63: 0.005256888 -0.8090952 0.6096982 0.4091181
## 64: 0.005256888 -0.8090952 0.6096982 0.4091181
## 65: 0.005256888 -0.8090952 0.6096982 0.4091181
## 66: 0.005256888 -0.8090952 0.6096982 0.4091181
## 67: 0.005256888 -0.8090952 0.6096982 0.4091181
## 68: 0.003699662 -1.7457057 0.5965758 0.2636889
## 69: 0.003699662 -1.7457057 0.5965758 0.2636889
## 70: 0.003699662 -1.7457057 0.5965758 0.2636889
## 71: 0.003699662 -1.7457057 0.5965758 0.2636889
## 72: 0.003699662 -1.7457057 0.5965758 0.2636889
## 73: 0.003699662 -1.7457057 0.5965758 0.2636889
## 74: 0.003612836 -1.5562853 0.3815687 0.4734673
## 75: 0.003612836 -1.5562853 0.3815687 0.4734673
## 76: 0.003612836 -1.5562853 0.3815687 0.4734673
## se.bp v c pchi
## [1] "ORF75" "ORF32" "ORF67_1" "ORF28" "ORF24" "ORF14" "ORF57"
## [8] "ORF76" "ORF62" "ORF63"## [1] 10## [1] "ORF1" "ORF4" "ORF9" "ORF18" "ORF20" "ORF21" "ORF31"
## [8] "ORF34" "ORF38" "ORF50" "ORF61" "NOIR_2" "ORF2" "ORF3"
## [15] "ORF8" "ORF11" "ORF22" "ORF26" "ORF29" "ORF36" "CTO"
## [22] "ORF40" "ORF73" "ORF5" "ORF65_1" "ORF69" "ORF10" "ORF15"
## [29] "ORF16" "ORF52" "ORF54" "ORF60" "ORF72" "ORF19" "ORF37"
## [36] "ORF51" "ORF66_1" "ORF76"## [1] 38Remove genes from clusters ?
## [1] "ORF1" "ORF4" "ORF9" "ORF18" "ORF20" "ORF21" "ORF31"
## [8] "ORF34" "ORF38" "ORF50" "ORF61" "NOIR_2" "ORF2" "ORF3"
## [15] "ORF8" "ORF11" "ORF22" "ORF26" "ORF29" "ORF36" "CTO"
## [22] "ORF40" "ORF73" "ORF5" "ORF65_1" "ORF69" "ORF10" "ORF15"
## [29] "ORF16" "ORF52" "ORF54" "ORF60" "ORF72" "ORF19" "ORF37"
## [36] "ORF51" "ORF66_1" "ORF76"## [1] 38## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 1 12
## 2: 2 11
## 3: 5 9
## 4: 7 9
## 5: 8 7
## 6: 9 6
## 7: 11 6
## 8: 10 5
## 9: 4 4
## 10: 3 3
## 11: 12 3
## 12: 6 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
